miRVaS

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Installation

Downloads

Program

• miRVaS-1.0.2-Windows-intel.zip
• miRVaS-1.0.2-Linux-i686.tar.gz

Supporting Files

• genome_hg19.ifas.zip
• genome_hg38.ifas.zip
• mir_mm10_mirbase21.tsv
• genome_mm10.ifas.zip

Older Versions

• miRVaS-1.0.1-Windows-intel.zip
• miRVaS-1.0.1-Linux-i686.tar.gz
• miRVaS-1.0.0-Windows-intel.zip
• miRVaS-1.0.0-Linux-i686.tar.gz

System Requirements

Java must be installed on the system for the drawing program to work.

The Linux version is 32 bit (Linux-i686). This is usually also supported on 64bit systems, although it may be necessary on 64bit systems to install the requested libraries (e.g. on Ubuntu Linux using the command sudo apt-get install ia32-libs libc6-i386 lib32gcc1).

Install

The miRVaS application itself does not need to be installed. After unpacking, it can be used directly by starting the mirvas executable in the unpacked directory. This executable must however stay in this application directory to work. If you want to be able to start it from another location (desktop, bin), make a link to it.

The program will search for the java executable, but if it does not find it, its location can be specified in the settings.txt file.

Two human miRNA databases are already included in the directory apps/mirvas/Databases:

• mirna_hg19_mirbase20.tsv
• mirna_hg38_mirbase21.tsv

miRVaS also needs a genome sequence (in fasta format with single line sequences) and a genome index file. This is not included with the program due to its size. The human genome sequence and index can be downloaded from this page (top), and preferentially put in the same Databases directory after uncompressing. miRNA data and genomes for other species can be downloaded and converted as described in the manual using the miRVaS convert option.

Example input files can be found in the examples directory.

Uninstalling is done by simply removing the directory.

Installing Other miRNA Databases

In order to run on another miRNA database (e.g. other species), miRVaS needs a genomefile and a miRNA datbase file.

• The genomefile must be in the FASTA format but with only one line per sequence. A fasta file given will be converted and indexed upon first use.
• Using the included conversion tool the miRNA database file can (e.g.) be generated based on the gff3 files per species and the miRNA.str file that you can download from miRBase (described more extensively in the manual).